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karel-brinda
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Phylign
Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)
http://brinda.eu/mof
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Add support for databases
#268
karel-brinda
opened
3 months ago
0
Modify to work on 2KK and remove download rules
#267
Danderson123
closed
5 months ago
0
Docs make format
#266
karel-brinda
closed
6 months ago
0
Failed to run with custom data
#265
shenwei356
opened
6 months ago
4
LFS cluster mode: only snakemake 7.32.4 worked, 6.x or 8.x failed.
#264
shenwei356
opened
6 months ago
1
new command 'make label' assign a label to query draft assembly based on the best hits from COBS
#263
jorgeavilacartes
opened
6 months ago
0
make download has no option to download the whole 661K database.
#262
shenwei356
closed
6 months ago
1
fix readme
#261
shenwei356
closed
6 months ago
1
Update README.md
#260
karel-brinda
closed
6 months ago
0
Add support for gzipped input files
#259
karel-brinda
opened
6 months ago
0
Tests are currently failing
#258
karel-brinda
closed
6 months ago
1
Update README.md
#257
karel-brinda
closed
6 months ago
0
ValueError: not enough values to unpack (expected 2, got 1)
#256
karel-brinda
closed
6 months ago
2
Add shields to readme
#255
karel-brinda
closed
9 months ago
0
Make download.sh robust and testable
#254
karel-brinda
closed
9 months ago
0
fix: fix number of download threads reportedly being 1 on some machines regardless of the configuration
#253
leoisl
closed
9 months ago
1
Improve `make help` interface and output
#252
karel-brinda
closed
9 months ago
0
Update colors of comments
#251
karel-brinda
closed
9 months ago
0
fix: filter out empty lines when getting the batches
#250
leoisl
closed
9 months ago
0
Fix "ANSI colors in Make Help command are not being interpreted"
#249
Francii-B
closed
9 months ago
4
ANSI colors in Make Help command are not being interpreted
#248
Francii-B
closed
9 months ago
4
Fix/236 (fix Zenodo blocking downloads)
#247
leoisl
closed
9 months ago
4
Decompressing COBS indexes takes way too much RAM
#246
leoisl
closed
9 months ago
1
Add `make download_asms` and `make download_cobs`
#245
Francii-B
closed
9 months ago
0
Add separate subcommands for downloading assemblies and cobs indexes
#244
Francii-B
closed
9 months ago
0
Task1
#243
Francii-B
closed
9 months ago
0
Number of download threads reportedly being 1 on some machines regardless of the configuration
#242
karel-brinda
closed
9 months ago
12
Update documentation
#241
karel-brinda
closed
9 months ago
0
Sometimes snakefmt breaks syntax for lambda functions
#240
karel-brinda
closed
9 months ago
0
Update directory structure & fix readme accordingly
#239
karel-brinda
closed
9 months ago
0
Update documentation
#238
karel-brinda
closed
9 months ago
0
fix: fewer concurrent downloads so that Zenodo does not start blocking downloads
#237
leoisl
closed
9 months ago
0
Zenodo is blocking some downloads
#236
leoisl
closed
9 months ago
20
fix: fix download issues and re-enables CI on ubuntu and mac and several python versions
#235
leoisl
closed
9 months ago
1
Downloading is not working and `make test` fails
#234
leoisl
closed
9 months ago
6
Add channels to conda command
#233
karel-brinda
closed
9 months ago
0
Update documentation
#232
karel-brinda
closed
10 months ago
0
Add a possibility to plug another mapper
#231
karel-brinda
opened
10 months ago
0
Fix a typo
#230
karel-brinda
closed
1 year ago
0
Update readme
#229
karel-brinda
closed
1 year ago
0
Update readme
#228
karel-brinda
closed
1 year ago
0
Fix max_download_threads in cluster mode
#227
leoisl
closed
9 months ago
2
Adds functionality to run MOF search in a LSF cluster
#226
leoisl
closed
1 year ago
1
batch_align.py loads up the whole query fasta into RAM
#225
leoisl
opened
1 year ago
2
Fix COBS filtering not properly taken into account and Minimap instances created even for 0 queries
#224
leoisl
closed
1 year ago
4
Minimap instances created even for 0 queries (COBS filtering not taken into account for mm2 instance building)
#223
karel-brinda
closed
1 year ago
2
Uses psutil to measure RAM, add a pipeline to check the truth kmer intersection with a query and other misc changes
#222
leoisl
closed
1 year ago
0
End of year and my updates
#221
leoisl
closed
1 year ago
0
Measuring pipeline's RAM usage with another method
#220
leoisl
closed
1 year ago
26
Verifying memory consumption measurements
#219
karel-brinda
closed
1 year ago
8
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